Tsumugi cafe 本願寺 [Tsukiji]
Kanetanaka So 金田中 草 [Shibuya]
Kanetanaka has large windows and white walls. The clean-lined, bright interior creates an energizing atmosphere. You can enjoy one of the best kaiseki traditional Japanese breakfast there. It comes with many small dishes of seasonal ingredients. Everything is so carefully prepared and presented. Very worth the go! Kanetanaka is a high-end restaurant where you can have luxurious courses of over ¥20,000 for dinner, but go there for breakfast and you can enjoy an exquisite meal for about ¥4,000.
The restaurant is located at a 4-minute walk of the South Exit of the JR Shibuya Station. It's on the 2nd floor of the Cerulean Tower Tokyu Hotel.
Breakfast time is from 7:00～10:30.
Shunsai 旬彩 [Shibuya]
Shunsai is another restaurant in Shibuya that is very worth the go for their traditional Japanese breakfasts. Located on the 25th floor of the Shibuya Excel Hotel Tokyo, it has a stunning view of the city. The breakfast sets are around ¥3,000 and come with the season's fish and vegetables.
The Shibuya Excel hotel is located a 2-minute walk from the Shibuya Station.
Breakfasts are from 7：00～10：30.
O-dashi Tokyo おだし東京 [Shinagawa]
"O-dashi" is the Japanese word for soup stock. So, you've probably guessed it, this restaurant specializes in Japanese-style soups and porridges that are full of natural umami. To make some of their dishes, they use a combination of up to nine different ingredients found in Japanese cuisine. The deep savoury broth comes from seaweed, dried fish, shiitake mushrooms, etc. O-dashi sets are around ¥1,000.
The restaurant is very near the Shinagawa Station.
Breakfast time is from 7:00〜11:00(8:00〜10:00 on Sunday and national holidays).
Shinpachi Shokudo しんぱち食堂 [Shinjuku]
Shinpachi Shokudo is a small restaurant of long standing in Shinjuku. It specializes in charcoal-grilled fish, which is the most quintessential food of the traditional Japanese breakfast along with the miso soup. They have about 20 different variations of set meals under ¥1,000. The cheapest one, which also is one of the most popular, is the grilled sardine set at ¥540, which comes with three fish.
The popular restaurant is at about a 3-minute walk from the West Exit of the Shinjuku Station.
Opens at 7:00.
Yaesu Hatsufuji やえす初藤 [Tokyo Station]
Yaesu Hatsufuji is an old-fashion traditional restaurant that is quite large with some 130 seats. You'll love the quaint atmosphere and the traditional Japanese breakfast special sets that start at around ¥500. They have displays of the sets on the storefront so you can have a good idea of what you'll take before walking in. Their breakfast set with a traditional savoury and fluffy Japanese omelette is the most popular option in the morning. You can add some tuna sashimi to that and your order won't go over ¥1,000. This is definitely one of the best places in Tokyo for an affordable Japanese breakfast.
Yesu Hatsufuji is located at about a 3-minute walk from the Tokyo Station, inside the Yaesu Shopping Mall which is directly connected to the Tokyo Station.
These restaurants are very well regarded by the locals for traditional breakfast cuisine. You probably won't regret going there. If you're looking later on for some good Japanese cuisine for lunch, the guide below might interest you as well.